It's just quirky to me that this happens and you have to do these conversions before the device will recognize the covers.

The problem is that the IDPF didn't think it important enough to specify a standard for cover images (although they will probably address this shortcoming in the next couple of years ). What is happening is that everyone comes up with their own heuristic for guessing the image. Calibre, Aldiko, Stanza, Nook, Nook Color ... they all determine the image using their own set of rules, but they don't generally share those rules so the next guy has to reinvent the wheel.

And, of course, the goal is to do as little work as possible (except Calibre which actually renders the first page of the book) because you generally have a battery-powered processor and Mobileread members that will try to put 3000 books on their device.